Database: PROSITE(DOC)
Entry: PDOC51192
LinkDB: PDOC51192
Original site: PDOC51192 
* Superfamilies 1 and 2 helicase domain profiles *

Helicases  have  been  classified in 5 superfamilies (SF1-SF5) [1]. All of the
proteins  bind ATP and, consequently, all of them carry the classical Walker A
(phosphate-binding   loop   or   P-loop)   (see   <PDOC00017>)  and  Walker  B
(Mg2+-binding  aspartic acid) motifs [1]. For the two largest groups, commonly
referred  to  as  SF1 and SF2, a total of seven characteristic motifs has been
identified  [2].  These  two superfamilies encompass a large number of DNA and
RNA helicases from archaea, eubacteria, eukaryotes and viruses that seem to be
active  as  monomers  or  dimers.  RNA  and DNA helicases are considered to be
enzymes  that  catalyze  the separation of double-stranded nucleic acids in an
energy-dependent manner [3].

The various structures of SF1 and SF2 helicases present a common core with two
alpha-beta   RecA-like   domains  (see  for  example  <PDB:1FUU>)  [3,4].  The
structural  homology  with  the  RecA  recombination  protein  covers the five
contiguous  parallel  beta  strands and the tandem alpha helices. ATP binds to
the  amino proximal alpha-beta domain, where the Walker A (motif I) and Walker
B (motif  II) are found. The N-terminal domain also contains motif III (S-A-T)
which  was  proposed to participate in linking ATPase and helicase activities.
The  carboxy-terminal  alpha-beta  domain  is structurally very similar to the
proximal  one even though it is bereft of an ATP-binding site, suggesting that
it may have originally arisen through gene duplication of the first one.

Some members of helicase superfamilies 1 and 2 are listed below:

 - DEAD-box  RNA  helicases  (see  <PDOC00039>).  The  prototype  of  DEAD-box
   proteins  is  the translation initiation factor eIF4A. The eIF4A protein is
   an  RNA-dependent  ATPase  which  functions  together  with eIF4B as an RNA
   helicases [5].
 - DEAH-box  RNA  helicases (see <PDOC00039>). Mainly pre-mRNA-splicing factor
   ATP-dependent RNA helicases [5].
 - Eukaryotic   DNA  repair  helicase RAD3/ERCC-2, an ATP-dependent 5'-3'  DNA
   helicase involved in nucleotide excision repair of UV-damaged DNA.
 - Eukaryotic  TFIIH  basal transcription factor complex helicase XPB subunit.
   An  ATP-dependent 3'-5' DNA helicase which is a component of the core-TFIIH
   basal transcription factor, involved in nucleotide excision repair (NER) of
   DNA  and, when complexed to CAK, in RNA transcription by RNA polymerase II.
   It  acts  by  opening DNA either around the RNA transcription start site or
   the DNA.
 - Eukaryotic  ATP-dependent  DNA  helicase  Q. A DNA helicase that may play a
   role  in  the  repair  of DNA that is damaged by ultraviolet light or other
 - Eukaryotic  ATP-dependent  helicase  SNF2/RAD54.  A  group of ATP-dependent
   remodelling factors frequently found associated with histone deacetylases.
 - Bacterial  and  eukaryotic antiviral SKI2-like helicase. SKI2 has a role in
   the  3'-mRNA  degradation  pathway. It represses dsRNA virus propagation by
   specifically  blocking  translation of viral mRNAs, perhaps recognizing the
   absence of CAP or poly(A).
 - Bacterial  DNA-damage-inducible  protein  G  (DinG).  A  probable  helicase
   involved in DNA repair and perhaps also replication.
 - Bacterial  primosomal  protein  N'  (PriA).  PriA  protein  is one of seven
   proteins  that  make  up  the restart primosome, an apparatus that promotes
   assembly   of   replisomes   at  recombination  intermediates  and  stalled
   replication forks.
 - Bacterial  ATP-dependent  DNA  helicase  recG.  It  has  a critical role in
   recombination   and   DNA   repair.  It  helps  process  Holliday  junction
   intermediates  to  mature products by catalyzing branch migration. It has a
   DNA  unwinding  activity  characteristic  of a DNA helicase with a 3' to 5'
 - ssRNA positive-strand  flaviviruses and potyviruses RNA helicase.
 - dsDNA viruses early transcription factor 70 kDa subunit.
 - dsDNA  viruses  nucleoside  triphosphatase I (NPH I) protein. It serves two
   roles   in  transcription;  it  acts  in  concert  with  viral  termination
   factor/capping enzyme to catalyze release of UUUUUNU-containing nascent RNA
   from  the  elongation  complex,  and  it  acts  by  itself  as a polymerase
   elongation factor to facilitate readthrough of intrinsic pause sites.
 - Poxviruses  transcript  release  DNA  helicase.  It  prevents virus-induced
   breakdown of RNA. It acts as a negative transcription elongation factor. It
   is involved in an ATP-dependent manner in release of nascent RNA.

To  recognize  helicase  Superfamilies 1 and 2 we have developed two profiles.
The  first one recognizes all classical SF1 and SF2 helicases except bacterial
DinG protein  and eukaryotic Rad3 which belong to the same subfamily and which
differ  from  other  SF1-SF2 helicases by the presence of a large insert after
the Walker A [6]. Our second profile recognizes specifically this subfamily.

-Sequences known to belong to this class detected by the first profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the second profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the third profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Note: UvrD (see <PDOC51198>) also belong to SF1 but is not picked-up by these
-Note:  secA  is  a  bacterial protein important for protein export which also
 contains  the seven motifs characteristic of SF1 and SF2. We also developed a
 profile specific for this family (see <PDOC01016>).

-Last update: April 2006 / First entry.

[ 1] Gorbalenya A.E., and Koonin E.V. .
     "Helicases: amino acid sequence comparisons and structure-function
     Curr. Opin. Struct. Biol. 3:419-429(1993).
[ 2] Gorbalenya A.E., Koonin E.V., Donchenko A.P., Blinov V.M.
     "Two related superfamilies of putative helicases involved in
     replication, recombination, repair and expression of DNA and RNA
     Nucleic Acids Res. 17:4713-4730(1989).
[ 3] Caruthers J.M., McKay D.B.
     "Helicase structure and mechanism."
     Curr. Opin. Struct. Biol. 12:123-133(2002).
[ 4] Caruthers J.M., Johnson E.R., McKay D.B.
     "Crystal structure of yeast initiation factor 4A, a DEAD-box RNA
     Proc. Natl. Acad. Sci. U.S.A. 97:13080-13085(2000).
     PubMed=11087862; DOI=10.1073/pnas.97.24.13080
[ 5] Tanner N.K., Linder P.
     "DExD/H box RNA helicases: from generic motors to specific
     dissociation functions."
     Mol. Cell 8:251-262(2001).
[ 6] Koonin E.V.
     "Escherichia coli dinG gene encodes a putative DNA helicase related to
     a group of eukaryotic helicases including Rad3 protein."
     Nucleic Acids Res. 21:1497-1497(1993).
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